Background: Mitoxantrone (MTX) is an immunosuppressive drug approved for multiple sclerosis (MS) treatment. Objective: The aim of this study is to evaluate and to compare the clinical and neuroradiological responses to MTX in relapsing-remitting (RR) and secondary progressive (SP) MS patients. Methods: We conducted a retrospective, non-randomized, open-label, observational study to evaluate the clinical and neuroradiological response to the drug in 79 patients with RR MS and 210 patients with SP MS. Results: A statistically significant reduction (p < 0.001) in the number of relapses was observed during MTX treatment and in the year after in both RR and SP MS patients. On the contrary, an opposite behavior in terms of disease progression was found in RR compared with SP MS patients, resulting in a statistically significant improvement of the Expanded Disability Status Scale score during the MTX treatment (p < 0.001) and in the year after (p < 0.001) for RR MS patients compared with a continuous, although mild, worsening of the disability in SP MS patients (p < 0.001). Finally, a significant reduction (p < 0.001) of new Gd-enhanced lesions in both RR and SP MS patients was observed in a subgroup of 224 individuals who underwent a brain MRI evaluation before and after MTX treatment. Conclusions: MTX should be considered as an effective therapeutic option in RR MS patients with evidence of relevant disease activity, but the potential life-threatening adverse events and the overall benefit-risk ratio must be carefully evaluated at individual patient level.